The 100 trillion microorganisms that naturally live inside and on humans are estimated to outnumber human cells by a factor of ten. The Human Microbiome Project sponsored by the NIH seeks to better understand the effects these complex communities have on human physiology, nutrition, immunity and development. These bacteria play an important role in health and disease, but surprisingly little is known about them due to the inability to cultivate and study many of them. One way to study the human microbiome is to analyze the genes and genomes of each member of the population. The SBIR Phase I grant proposal "Massively Parallel Single Cell Genomics of the Human Microbiome" seeks to develop high throughput methods for isolating large numbers of individual microbial cells, amplifying the genomes of single microbial cells and constructing clone-free libraries for sequence analysis on a numerically large scale. These goals will be achieved by developing DNA amplification tools that simplify single-cell genomics, dramatically improving the efficiency of existing clone-free library construction methods, and integrating these methods with a new droplet based platform for manipulating single cells and their genomes. A new thermostable phage DNA polymerase that rapidly and efficiently amplifies DNA at high temperature overcomes numerous technical challenges for single cell genomics. A new method that improves the construction of sequencing libraries by two orders of magnitude will simplify and accelerate the analysis of these genomes. A new droplet based microfluidic reaction device that precisely controls the manipulation and screening of single cells, improves the amplification efficiency of single molecules and enables the parallel processing of 10 million droplets per experiment promises to accelerate the development of numerous biomolecular methods. The long term goal of the proposal is to refine and integrate these tools and instruments in order to study the human microbiome on a scale that is tractable. PUBLIC HEALTH RELEVANCE: The SBIR Phase I grant proposal "Massively Parallel Single Cell Genomics of the Human Microbiome" seeks to integrate new tools and technologies to analyze the genes and genomes of the trillions of microbes that live in and on humans. Outcomes that can be predicted include new diagnostic biomarkers of health, a twenty-first century pharmacopoeia that includes members of the human microbiota and the chemical messengers they produce, industrial applications based on enzymes that are produced by the human microbiota, and a deeper understanding of the nutritional requirements of humans. The ability to correlate particular genes or genomes with a disease state will also be relevant to public health. [unreadable] [unreadable] [unreadable]